Issue 30: Specifying the enzyme rules used in the search
http://code.google.com/p/psi-pi/issues/detail?id=30
Comment #37 by eisenachM:
Two possible variants for encoding regular expressions
for the default enzymes into the OBO file:
1) "xref" and 2) "has_a" relationship.
[Term]
id: PI:00251
name: Trypsin
xref_analog: regexp:(?<=[KR\])(?\!P)
is_a: PI:00045 ! cleavage agent name
relationship: has_a PI:00176 ! (?<=[KR])(?!P)
For the 1st variant, the regular expression is only a string.
For the 2nd variant, the regular expression is itself a
term (PI:00176) and child of a "regular expression" term.
Both methods have disadvantages:
In OBOEdit the xref gives a warning, because it contains non-URI characters.
In OBOEdit the has_a relationship is not shown in the tree view, but only in
the Parent Plugin (see screenshot attached).
Which do we prefer?
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